I am planning a metatranscriptomic experiment on sludge samples. I have extracted RNA from a number of different bacteria but I have never performed metatranscriptomic analysis in the past.
Does anyone have any suggestions on a good kit or protocol to isolate RNA from a microbial community and to perform rRNA depletion?
Thank you
Http://www.mobio.com/soil-rna-isolation/rna-powersoil-total-rna-isolation-kit.html
In my opinion ZR Soil/Fecal RNA Kits, will also yield good quality of product. ALL THE VERY BEST DOCTOR
Using kits is fine but very difficult to troubleshoot if the extraction is unsuccessful as you will not known what in reagents are used in the kit. However, as the answers below suggest they do usually work.
If you want a bespoke method they I developed a very effective RNA extraction method in the 1990s, see Purdy et al 1996 Appl Environ Microbiol 62: 3905-3907 or a more detailed extraction chapter Purdy 2005 Meths Enzymol 397: 271-292.
As for rRNA depletion some of the most successful work in this area is by either Mary-Ann Moran's or David Karl's groups. These aren't on sludge so you will face different issues of contamination but the basic principles once you have good clean RNA are the same.
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